{"id":"https://openalex.org/W4411370561","doi":"https://doi.org/10.1021/acs.jcim.5c00969","title":"HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes","display_name":"HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes","publication_year":2025,"publication_date":"2025-06-17","ids":{"openalex":"https://openalex.org/W4411370561","doi":"https://doi.org/10.1021/acs.jcim.5c00969","pmid":"https://pubmed.ncbi.nlm.nih.gov/40526044"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00969","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00969","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c00969","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046328622","display_name":"Marco Giulini","orcid":"https://orcid.org/0000-0002-2691-712X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marco Giulini","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071040806","display_name":"Victor Reys","orcid":"https://orcid.org/0000-0001-5301-317X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Victor Reys","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052389219","display_name":"Jo\u00e3o M. C. Teixeira","orcid":"https://orcid.org/0000-0002-9113-0622"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o M. C. Teixeira","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","Zymvol Biomodeling, Carrer de Pau Claris 94, 3B, 08010 Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Zymvol Biomodeling, Carrer de Pau Claris 94, 3B, 08010 Barcelona, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012374366","display_name":"Brian Jim\u00e9nez\u2010Garc\u00eda","orcid":"https://orcid.org/0000-0001-7786-2109"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Brian Jim\u00e9nez-Garc\u00eda","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","Zymvol Biomodeling, Carrer de Pau Claris 94, 3B, 08010 Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Zymvol Biomodeling, Carrer de Pau Claris 94, 3B, 08010 Barcelona, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073057216","display_name":"Rodrigo V. Honorato","orcid":"https://orcid.org/0000-0001-5267-3002"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rodrigo V. Honorato","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074321101","display_name":"Anna Kravchenko","orcid":"https://orcid.org/0000-0002-2332-4206"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anna Kravchenko","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101454232","display_name":"Xiaotong Xu","orcid":"https://orcid.org/0009-0006-1883-6692"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Xiaotong Xu","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092608027","display_name":"Rapha\u00eblle Versini","orcid":"https://orcid.org/0000-0002-1390-4354"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rapha\u00eblle Versini","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083327350","display_name":"Anna Engel","orcid":"https://orcid.org/0009-0002-1806-7951"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anna Engel","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046925828","display_name":"Stefan Verhoeven","orcid":"https://orcid.org/0000-0002-5821-2060"},"institutions":[{"id":"https://openalex.org/I4210095242","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800991832","https://openalex.org/I4210090210","https://openalex.org/I4210095242"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Stefan Verhoeven","raw_affiliation_strings":["Netherlands eScience Center, Science Park 402, 1098 XH Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Netherlands eScience Center, Science Park 402, 1098 XH Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210095242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alexandre M. J. J. Bonvin","raw_affiliation_strings":["Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Bijvoet Centre for Biomolecular Research, Faculty of Science\u2500Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5064072429"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":null,"apc_paid":null,"fwci":13.3994,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.99110173,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"65","issue":"13","first_page":"7315","last_page":"7324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7750511169433594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46087390184402466},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.36369940638542175},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3595806956291199},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3374241888523102},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.14878594875335693},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12805339694023132},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12762680649757385}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7750511169433594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46087390184402466},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.36369940638542175},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3595806956291199},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3374241888523102},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.14878594875335693},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12805339694023132},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12762680649757385}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c00969","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00969","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40526044","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40526044","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12264957","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12264957","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00969","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00969","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5029271195","display_name":null,"funder_award_id":"027.020.G13","funder_id":"https://openalex.org/F4320314239","funder_display_name":"Netherlands eScience Center"},{"id":"https://openalex.org/G7673258202","display_name":null,"funder_award_id":"BioExcel / 823830","funder_id":"https://openalex.org/F4320338448","funder_display_name":"HORIZON EUROPE European Innovation Council"}],"funders":[{"id":"https://openalex.org/F4320314239","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475"},{"id":"https://openalex.org/F4320338448","display_name":"HORIZON EUROPE European Innovation Council","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1948562438","https://openalex.org/W2010612779","https://openalex.org/W2014957977","https://openalex.org/W2018410079","https://openalex.org/W2021374144","https://openalex.org/W2030728145","https://openalex.org/W2032592607","https://openalex.org/W2077834136","https://openalex.org/W2101636319","https://openalex.org/W2110968143","https://openalex.org/W2117672117","https://openalex.org/W2131654992","https://openalex.org/W2137167381","https://openalex.org/W2153983456","https://openalex.org/W2154019529","https://openalex.org/W2171356751","https://openalex.org/W2508425869","https://openalex.org/W2753374271","https://openalex.org/W2890113953","https://openalex.org/W2909255640","https://openalex.org/W2950365860","https://openalex.org/W2953103783","https://openalex.org/W2978232173","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3202105508","https://openalex.org/W3216616254","https://openalex.org/W4220824576","https://openalex.org/W4286669150","https://openalex.org/W4309862248","https://openalex.org/W4310159409","https://openalex.org/W4327550249","https://openalex.org/W4385798891","https://openalex.org/W4388946853","https://openalex.org/W4390640808","https://openalex.org/W4392544734","https://openalex.org/W4396721167","https://openalex.org/W4399731408","https://openalex.org/W4401339769","https://openalex.org/W4403099076","https://openalex.org/W4404292709","https://openalex.org/W4405886344"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"HADDOCK":[0],"is":[1,16,132],"a":[2,10,57,86],"widely":[3],"used":[4],"resource":[5],"for":[6],"integrative":[7,82],"modeling":[8,83],"of":[9,12,40,59,108,111,121],"variety":[11],"biomolecular":[13],"complexes":[14],"that":[15,113],"able":[17],"to":[18,73,90],"incorporate":[19],"experimental":[20],"knowledge":[21],"into":[22,56],"physics-based":[23,88],"calculations":[24],"during":[25],"complex":[26],"prediction,":[27],"refinement,":[28],"scoring":[29],"and":[30,62,69,92,140],"analysis.":[31],"Here":[32],"we":[33],"introduce":[34],"HADDOCK3,":[35],"the":[36,41,45,94,102,118,136],"new":[37],"modular":[38],"version":[39],"program,":[42],"in":[43,101,152],"which":[44],"original,":[46],"parametrizable":[47],"albeit":[48],"rigid":[49],"pipeline":[50],"has":[51],"been":[52],"first":[53],"broken":[54],"down":[55],"catalogue":[58],"independent":[60],"modules":[61],"then":[63],"enriched":[64],"with":[65,117,142],"powerful":[66],"analysis":[67],"tools":[68],"third-party":[70],"integrations.":[71],"Thanks":[72],"this":[74,153],"increased":[75],"flexibility,":[76],"HADDOCK3":[77,112,128],"can":[78],"now":[79],"handle":[80],"multiple":[81],"scenarios,":[84],"providing":[85],"valuable,":[87],"tool":[89],"enrich":[91],"complement":[93],"predictions":[95],"made":[96],"by":[97],"machine":[98],"learning":[99],"algorithms":[100],"post-AlphaFold":[103],"era.":[104],"We":[105],"present":[106],"examples":[107],"successful":[109],"applications":[110],"were":[114],"not":[115],"feasible":[116],"previous":[119],"versions":[120],"HADDOCK,":[122],"highlighting":[123],"its":[124],"expanded":[125],"capabilities.":[126],"The":[127],"software":[129],"source":[130],"code":[131],"freely":[133],"available":[134,156],"from":[135],"GitHub":[137],"repository":[138],"(https://github.com/haddocking/haddock3)":[139],"comes":[141],"an":[143],"online":[144],"user":[145],"guide":[146],"(www.bonvinlab.org/haddock3-user-manual).":[147],"All":[148],"example":[149],"data":[150],"described":[151],"manuscript":[154],"are":[155],"at":[157],"https://github.com/haddocking/haddock3-paper-data.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}
